The royals embarked on an amphibious sightseeing tour on the Yellow Duckmarine, a sailing vessel based on original WWII vehicles.
The couple were shown the sights around Salthouse and Albert Docks before heading to the Maritime Museum.
"It is a true honour to welcome The Queen and The Duke of Edinburgh to Liverpool," said Yellow Duckmarine managing director Jerry Goldman.
"We hope that Her Majesty enjoyed her tour and that she felt the warm welcome to our city and its wonderful attractions."
The Queen was visiting the area as part of her Diamond Jubilee Tour.